OmeSource¶
Module Contents¶
Classes¶
OME-compatible image source (base class) |
Functions¶
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- class OmeSource.OmeSource¶
OME-compatible image source (base class)
- metadata: dict¶
metadata dictionary
- has_ome_metadata: bool¶
has ome metadata
- dimension_order: str¶
source dimension order
- output_dimension_order: str¶
data dimension order
- source_pixel_size: list¶
original source pixel size
- target_pixel_size: list¶
target pixel size
- sizes: list¶
x/y size pairs for all pages
- sizes_xyzct: list¶
xyzct size for all pages
- pixel_types: list¶
pixel types for all pages
- pixel_nbits: list¶
#bits for all pages
- channels: list¶
channel information for all image channels
- position: list¶
source position information
- default_physical_unit = 'µm'¶
- _init_metadata(source_reference: str, source_pixel_size: list = None, target_pixel_size: list = None, source_info_required: bool = False)¶
- _get_ome_metadate()¶
- _init_sizes()¶
- abstract get_source_dask()¶
- get_mag() float¶
- get_dimension_order() str¶
- get_physical_size() tuple¶
- get_pixel_type(level: int = 0) numpy.dtype¶
- get_pixel_nbytes(level: int = 0) int¶
- get_channels() list¶
- get_size() tuple¶
- get_size_xyzct() tuple¶
- get_nchannels()¶
- get_pixel_size() list¶
- get_pixel_size_micrometer()¶
- get_shape(dimension_order: str = None, xyzct: tuple = None) tuple¶
- get_thumbnail(target_size: tuple, precise: bool = False) numpy.ndarray¶
- get_channel_window(channeli)¶
- render(image: numpy.ndarray, source_dimension_order: str = None, t: int = 0, z: int = 0, channels: list = []) numpy.ndarray¶
- asarray(pixel_size: list = [], **slicing) numpy.ndarray¶
- asarray_um(**slicing)¶
- asdask(chunk_size: tuple) dask.array.Array¶
- clone_empty() numpy.ndarray¶
- produce_chunks(chunk_size: tuple) tuple¶
- get_metadata() dict¶
- create_xml_metadata(output_filename: str, combine_rgb: bool = True, pyramid_sizes_add: list = None) str¶
- abstract _find_metadata()¶
- abstract _asarray_level(level: int, **slicing) numpy.ndarray¶
- close()¶
- OmeSource.get_resolution_from_pixel_size(pixel_size: list) tuple¶
- OmeSource.get_best_size(sizes: list, target_size: tuple) tuple¶